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Knots and Swelling in Protein Folding
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics.
2009 (English)Article in journal (Refereed) Submitted
Place, publisher, year, edition, pages
2009.
National Category
Subatomic Physics
Research subject
Theoretical Physics
Identifiers
URN: urn:nbn:se:uu:diva-287850OAI: oai:DiVA.org:uu-287850DiVA: diva2:923530
Note

Proteins can sometimes be knotted, and for many reasons the study of knotted proteins is rapidly becoming very important. For example, it has been proposed that a knot increases the stability of a protein. Knots may also alter enzymatic activities and enhance binding. Moreover, knotted proteins may even have some substantial biomedical significance in relation to illnesses such as Parkinson's disease. But to a large extent the biological role of knots remains a conundrum. In particular, there is no explanation why knotted proteins are so scarce. Here we argue that knots are relatively rare because they tend to cause swelling in proteins that are too short, and presently short proteins are over-represented in the Protein Data Bank (PDB). Using Monte Carlo simulations we predict that the figure-8 knot leads to the most compact protein configuration when the number of amino acids is in the range of 200-600. For the existence of the simplest knot, the trefoil, we estimate a theoretical upper bound of 300-400 amino acids, in line with the available PDB data.

Available from: 2016-04-26 Created: 2016-04-26 Last updated: 2016-04-26

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http://arxiv.org/abs/0906.4950

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Niemi, Antti
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